15-40611480-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BS1_Supporting
The NM_144508.5(KNL1):āc.253A>Gā(p.Thr85Ala) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000629 in 238,594 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_144508.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KNL1 | NM_144508.5 | c.253A>G | p.Thr85Ala | missense_variant, splice_region_variant | 7/26 | ENST00000399668.7 | |
KNL1 | NM_170589.5 | c.331A>G | p.Thr111Ala | missense_variant, splice_region_variant | 8/27 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KNL1 | ENST00000399668.7 | c.253A>G | p.Thr85Ala | missense_variant, splice_region_variant | 7/26 | 1 | NM_144508.5 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152130Hom.: 1 Cov.: 31
GnomAD3 exomes AF: 0.0000604 AC: 2AN: 33098Hom.: 0 AF XY: 0.000116 AC XY: 2AN XY: 17176
GnomAD4 exome AF: 0.0000347 AC: 3AN: 86346Hom.: 0 Cov.: 0 AF XY: 0.0000699 AC XY: 3AN XY: 42918
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152248Hom.: 1 Cov.: 31 AF XY: 0.000148 AC XY: 11AN XY: 74460
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | May 02, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at